A cell cycle-coordinated Polymerase II transcription compartment encompasses gene expression before global genome activation

Abstract

Most metazoan embryos commence development with rapid, transcriptionally silent cell divisions, with genome activation delayed until the mid-blastula transition (MBT). However, a set of genes escapes global repression and gets activated before MBT. Here we describe the formation and the spatio-temporal dynamics of a pair of distinct transcription compartments, which encompasses the earliest gene expression in zebrafish. 4D imaging of pri-miR430 and zinc-finger-gene activities by a novel, native transcription imaging approach reveals transcriptional sharing of nuclear compartments, which are regulated by homologous chromosome organisation. These compartments carry the majority of nascent-RNAs and active Polymerase II, are chromatin-depleted and represent the main sites of detectable transcription before MBT. Transcription occurs during the S-phase of increasingly permissive cleavage cycles. It is proposed, that the transcription compartment is part of the regulatory architecture of embryonic nuclei and offers a transcriptionally competent environment to facilitate early escape from repression before global genome activation.

Quantitative measurements of chromatin modification dynamics during zygotic genome activation

“…1c; Supplementary movie 2). In good agreement with previous reports (Chan et al, 2018;Hadzhiev et al, 2019), RNAP2 Ser2ph foci were co-localized with bright miR-430 Morpholino signals in living embryos, suggesting that the nuclear and local concentration of RNAP2 Ser2ph-Fab reports on transcription activity in living zebrafish embryos, even though the sensitivity may not be as high as the transcript-specific Morpholino, which binds stably to the target RNA compared to the transient binding of Fabs.…”

“…miR-430 family genes that play a role for clearance of maternal RNAs are expressed at the highest level among the early transcribed genes (Hadzhiev et al, 2019;Heyn et al, 2014). To confirm this notion, a Cy3-labeled Morpholino oligonucleotide that targets miR-430 transcripts (Hadzhiev et al, 2019) was injected with Alexa488-labeled RNAP2 Ser2ph-Fab into living embryos ( Fig. 1c; Supplementary movie 2).…”

“…These foci were likely to contain alleles of miR-430 gene clusters on chromosome 4 (Chan et al, 2018;Giraldez et al, 2006;Hadzhiev et al, 2019;Heyn et al, 2014;Hilbert et al, 2018). miR-430 family genes that play a role for clearance of maternal RNAs are expressed at the highest level among the early transcribed genes (Hadzhiev et al, 2019;Heyn et al, 2014).…”

Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation

“…We find that the mir-430 cluster, which is transcribed two orders of magnitude higher than any other region, undergoes a dramatic loss in accessibility when elongation of RNA polymerase II is blocked. The miR-430 cluster is one of the first to be transcribed and initially, all transcribing RNA polymerase II localizes to the two alleles of the miR-430 cluster [19][20][21]56], which might facilitate the formation of RNA-pol II 'trains' capable of evicting nucleosomes, as shown in vitro [33].…”

The nuclear to cytoplasmic ratio directly regulates zygotic transcription inDrosophilathrough multiple modalities

“…1995; Hadzhiev et al, 2019;Müller et al, 2001). In Drosophila and zebrafish, it has been observed that the majority of the early transcripts are short and lack introns, leading to the suggestion that the early interphases simply are not long enough to sustain robust transcription of most genes (McKnight and Miller, 1976;Shermoen and O'Farrell, 1991;Rothe et al, 1992;De Renzis et al, 2007;Chen et al, 2013;Heyn et al, 2014;Kwasnieski et al, 2019).…”